MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : orot_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (13 of 14: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b2242 b3553 b3846 b2341 b1241 b0351 b4069 b4384 b2297 b2458 b2926 b0030 b2407 b1612 b1611 b4122 b0907 b3962 b0104 b3616 b3589 b4267 b1033 b0675 b1415 b1014 b0261 b0822 b4138 b4123 b0621 b4381 b2406 b0112 b2868 b0114 b0529 b2492 b0904 b3028 b1380 b0325 b4042 b4266 b3662 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.307847 (mmol/gDw/h)
  Minimum Production Rate : 0.891184 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 34.701427
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.058725
  EX_pi_e : 0.296952
  EX_so4_e : 0.077522
  EX_k_e : 0.060090
  EX_fe2_e : 0.004944
  EX_mg2_e : 0.002671
  EX_ca2_e : 0.001602
  EX_cl_e : 0.001602
  EX_cu2_e : 0.000218
  EX_mn2_e : 0.000213
  EX_zn2_e : 0.000105
  EX_ni2_e : 0.000099

Product: (mmol/gDw/h)
  EX_h2o_e : 51.785137
  EX_co2_e : 30.903700
  EX_h_e : 12.980114
  EX_ac_e : 1.522824
  EX_succ_e : 1.501673
  Auxiliary production reaction : 0.891184
  EX_ade_e : 0.590326
  EX_dxylnt_e : 0.000137
  DM_5drib_c : 0.000069
  DM_4crsol_c : 0.000069

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

Last updated: 21-Sep-2023
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